[BioC] problems reading Illumina files using BeadExplorer

Vitalina Komashko vmkomashko at ucdavis.edu
Thu Oct 26 02:30:20 CEST 2006


Dear all,
I am trying to use BeadExplorer to load Illumina Mouse8 arrays for 
analysis.
I used the latest BeadStudio software version to generate expression 
data, but it actually does not give summary  files such as 
gene.profile.csv and qcinfo.csv, so I had to save them separately when I 
opened the data. Here the error I constantly get when I load the data:
 > data<-beadAnalysis()
Read C:/Program Files/R/R-2.4.0/data/mouse_copy_sample_gene_profile.csv
Normalised data...
Generated qc data...
Error in sum(detExprs(beadData)[, i] > value) :
        subscript out of bounds
In addition: Warning message:
no non-missing arguments to min; returning Inf

There are no header lines when I save my data directly from BeadStudio. 
Does it matter?

R info:
 > sessionInfo()
R version 2.4.0 (2006-10-03)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "tools"     "tcltk"     "methods"   "stats"     "graphics"  "grDevices"
[7] "utils"     "datasets"  "base"    

other attached packages:
     convert       marray        limma BeadExplorer    tkWidgets       
DynDoc
     "1.8.0"     "1.12.0"      "2.9.1"      "1.2.0"     "1.12.0"     
"1.12.0"
      R2HTML         affy       affyio  widgetTools      Biobase
      "1.58"     "1.12.0"      "1.2.0"     "1.10.0"     "1.12.1"

I will appreciate any help. Thank you!
Vitalina.



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